Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver.

Frontiers in Cell and Developmental Biology
Xianliang HouYong Dai

Abstract

The liver is one of vital organs of the human body, and it plays an important role in the metabolism and detoxification. Moreover, fetal liver is one of the hematopoietic places during ontogeny. Understanding how this complex organ develops during embryogenesis will yield insights into how functional liver replacement tissue can be engineered and how liver regeneration can be promoted. Here, we combine the advantages of single-cell RNA sequencing and Spatial Transcriptomics (ST) technology for unbiased analysis of fetal livers over developmental time from 8 post-conception weeks (PCW) and 17 PCW in humans. We systematically identified nine cell types, and defined the developmental pathways of the major cell types. The results showed that human fetal livers experienced blood rapid growth and immigration during the period studied in our experiments, and identified the differentially expressed genes, and metabolic changes in the developmental process of erythroid cells. In addition, we focus on the expression of liver disease related genes, and found that 17 genes published and linked to liver disease mainly expressed in megakaryocyte and endothelial, hardly expressed in any other cell types. Together, our findings provide a compr...Continue Reading

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References

Nov 17, 1990·BMJ : British Medical Journal·D J Barker
Sep 16, 2005·European Journal of Immunology·Andreas LimmerPercy A Knolle
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Bin Zhang, Steve Horvath
Nov 15, 2011·Nature Biotechnology·Piero DalerbaStephen R Quake
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Sep 18, 2013·Blood Cells, Molecules & Diseases·Rachel Golub, Ana Cumano
Jul 16, 2014·Cell Stem Cell·Josien C van WolfswinkelPeter W Reddien
Sep 28, 2014·Bioinformatics·Simon AndersWolfgang Huber
Apr 14, 2015·Nature Biotechnology·Rahul SatijaAviv Regev
Jun 18, 2015·Development·Miriam GordilloValerie Gouon-Evans
Feb 19, 2016·Journal of Molecular Endocrinology·Philip A Gruppuso, Jennifer A Sanders
Jul 6, 2017·Development·Andrejs IvanovsAlexander Medvinsky
Oct 13, 2017·Scientific Reports·Michaela AspJoakim Lundeberg
Dec 7, 2017·World Journal of Gastroenterology : WJG·Yao NiWen-Liang Lv
Mar 2, 2018·Blood Advances·Shahrouz GhafooryJasimuddin Ahamed
Jun 1, 2018·Neonatology·Umberto SimeoniJean-François Tolsa
Jun 22, 2018·Nature Communications·Emelie BerglundJoakim Lundeberg
Jun 24, 2018·Science China. Life Sciences·Suwei Gao, Feng Liu
Mar 14, 2019·Seminars in Reproductive Medicine·Olivia J CarpinelloMicah J Hill
Oct 11, 2019·Nature·Dorin-Mirel PopescuMuzlifah Haniffa

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Software Mentioned

STAR
MIA
Spatial Transcriptomics ( ST
circlize
Bowtie2
CellCycleScoring
Cell Ranger Single - Cell Software Suite
count
htseq
Space Ranger

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